Riverine input often leads to high biological productivity in coastal areas. In coastal areas termed as region of freshwater influence (ROFI), horizontal anticyclonic gyres and vertical circulation form by density differences between buoyant river water and sea water. Previous physical oceanography studies have shown that the horizontal pattern of anticyclonic gyres and the strength of vertical circulation are dependent on the bottom topography of ROFI. However, the dependencies of biogeochemical cycles such as the net primary production (NPP) on the bottom topography have not been verified. In order to clarify how the bottom topography affects the NPP in phytoplankton blooms caused by riverine input through the physical processes in ROFI, we used an ocean general circulation model (OGCM) including a simple ecosystem model and conducted several case studies varying the bottom slope angle in the ideal settings. We estimated NPP categorized into three nutrients supplied from the river, the sea-subsurface layer and via regeneration: RI-NPP, S-NPP and RE-NPP. S-NPP and RE-NPP are larger and smaller with a steeper slope, respectively, while RI-NPP is not affected by the slope angle. As a result, total NPP is weakly dependent on the slope angle, i.e., because S- and RE-NPPs cancel each other out through two physical processes, (1) S-NPP is controlled by the strength of the vertical circulation and (2) RE-NPP is controlled by the shape of the horizontal gyre, which both vary with the bottom slope angle. We also conducted realistic simulations for Ishikari Bay, Japan and confirmed a similar dependency to that in the above ideal settings. That is, the simulation results are consistent with the regime of ideal settings and show that RI and RE-NPPs are important variables for Ishikari Bay which has a gentle slope. (C) 2016 The Authors. Published by Elsevier Ltd.